The Stokes-Einstein Relation at Moderate Schmidt Number

The Stokes-Einstein relation for the self-diffusion coefficient of a spherical particle suspended in an incompressible fluid is an asymptotic result in the limit of large Schmidt number, that is, when momentum diffuses much faster than the particle. When the Schmidt number is moderate, which happens in most particle methods for hydrodynamics, deviations from the Stokes-Einstein prediction are expected. We study these corrections computationally using a recently-developed minimally-resolved method for coupling particles to an incompressible fluctuating fluid in both two and three dimensions. We find that for moderate Schmidt numbers the diffusion coefficient is reduced relative to the Stokes-Einstein prediction by an amount inversely proportional to the Schmidt number in both two and three dimensions. We find, however, that the Einstein formula is obeyed at all Schmidt numbers, consistent with linear response theory. The numerical data is in good agreement with an approximate self-consistent theory, which can be used to estimate finite-Schmidt number corrections in a variety of methods. Our results indicate that the corrections to the Stokes-Einstein formula come primarily from the fact that the particle itself diffuses together with the momentum. Our study separates effects coming from corrections to no-slip hydrodynamics from those of finite separation of time scales, allowing for a better understanding of widely observed deviations from the Stokes-Einstein prediction in particle methods such as molecular dynamics.Comment: Submitte

Two-dimensional proteome reference map of Vibrio tapetis, the aetiological agent of brown ring disease in clams

Aims: Vibrio tapetis is the etiological agent of brown ring disease (BRD) in clams, one of the most threatening diseases affecting this commercially important bivalve. In this study we have constructed a proteome reference map of the V. tapetis type strain CECT 4600T. Methods and Results: Eighty-two proteins, consistently present in all 2D-gels, were identified by mass spectrometry or by de novo sequencing. The majority of the proteins identified (66%) belonged to four COG categories: 'Carbohydrate transport and metabolism', 'Post-translational modification, protein turnover and chaperones', 'Energy production', and 'Amino acid transport and metabolism'. Glyceraldehyde-3-phosphate dehydrogenase, enolase, fructose-bisphosphate aldolase, phosphoglycerate kinase. molecular chaperones Dnak and GroEL, alkyl hydroperoxide reductase, peptidyl-prolyl cis-trans isomerase B and factor Tu, were identified among the 20 most abundant proteins. A comparison of this reference map with that obtained for the V. tapetis strain GR0202RD, with different origin and pathophysiological characteristics, was performed. Conclusions: Under the culture conditions employed in this study, glucose degradation is one of the major pathways for energy production in Vibrio tapetis. In addition, the two strains studied, although with remarkable differences at genetic and pathophysiological levels, showed a high similarity under laboratory conditions. Significance and Impact of the Study: The results obtained here can be considered as a first step to gather valuable information on protein expression, related not only to diverse cellular functions and regulation but also to pathogenesis and bacterium-host interactions in the disease process

<i>Vibrio breoganii</i> sp. nov., a non-motile, alginolytic, marine bacterium within the <i>Vibrio halioticoli</i> clade

Seven non-motile, facultatively anaerobic, alginolytic marine bacteria were isolated from the cultured clams Ruditapes philippinarum and Ruditapes decussatus. Phylogenetic analysis based on 16S rRNA gene sequences showed that these marine bacteria were closely related to the recently described species Vibrio comitans, Vibrio rarus and Vibrio inusitatus (=99.0?% sequence similarity). Phylogenetic analysis based on the housekeeping genes rpoA, recA and atpA grouped the isolates together and allocated them to the Vibrio halioticoli species group. Amplified fragment length polymorphism DNA fingerprinting also grouped them together and enabled them to be differentiated from recognized species of the V. halioticoli clade. DNA–DNA hybridizations showed that the isolates belonged to a novel species; phenotypic features such as the ability to grow at 4 °C and in the presence of 6?% NaCl also enabled them to be separated from other species. The DNA G+C content of RD 15.11T is 44.4 mol%. The genotypic and phenotypic data showed that the isolates represent a novel species in the V. halioticoli clade. The name Vibrio breoganii sp. nov. is proposed, with RD 15.11T (=CECT 7222T =LMG 23858T) as the type strain

Mixed hydrogen-deuterium plasmas on JET ILW

A study of mixed hydrogen-deuterium H-mode plasmas has been carried out in JET-ILW to strengthen the physics basis for extrapolations to JET D-T operation and to support the development of strategies for isotope ratio control in future experiments. Variations of input power, gas fuelling and isotopic mixture were performed in H-mode plasmas of the same magnetic field, plasma current and divertor configuration. The analysis of the energy confinement as a function of isotope mixture reveals that the biggest change is seen in plasmas with small fractions of H or D, in particular when including pure isotope plasmas. To interpret the results correctly, the dependence of the power threshold for access to type-I ELMing H-modes on the isotope mixture must be taken into account. For plasmas with effective mass between 1.2 and 1.8 the plasma thermal stored energy (Wth) scales as m 0.1 eff, which is weaker than that in the ITER physics basis, IPB98 scaling. At fixed stored energy, deuterium-rich plasmas feature higher density pedestals, while the temperature at the pedestal top is lower, showing that at the same gas fuelling rate and power level, the pedestal pressure remains constant with an exchange of density and temperature as the isotope ratio is varied. Isotope control was successfully tested in JET-ILW by changing the isotope ratio throughout a discharge, switching from D to H gas puffing. Several energy confinement times (300 ms) are needed to fully change the isotope ratio during a discharge.EUROfusion Consortium Grant Agreement No. 633 053RCUK Energy Programme (Grant Number EP/I501 045)H2020 Marie-Sklodowska Curie programme (Grant No. 708 257)Spanish Ministry of Economy and Competitiveness (Grant No. FJCI-201 422 139

Correlation between Infrared Colors and Intensity Ratios of SiO Maser Lines

We present the results of SiO millimeter-line observations of a sample of known SiO maser sources covering a wide dust-temperature range. A cold part of the sample was selected from the SiO maser sources found in our recent SiO maser survey of cold dusty objects. The aim of the present research is to investigate the causes of the correlation between infrared colors and SiO maser intensity ratios among different transition lines. In particular, the correlation between infrared colors and SiO maser intensity ratio among the J=1-0 v=1, 2, and 3 lines are mainly concerned in this paper. We observed in total 75 SiO maser sources with the Nobeyama 45m telescope quasi-simultaneously in the SiO J=1-0 v=0, 1, 2, 3, 4 and J=2-1 v=1, 2 lines. We also observed the sample in the 29SiO J=1-0 v=0 and J=2-1 v=0, and 30SiO J=1-0 v=0 lines, and the H2O 6(1,6)-5(2,3) line. As reported in previous papers, we confirmed that the intensity ratios of the SiO J=1-0 v=2 to v=1 lines clearly correlate with infrared colors. In addition, we found possible correlation between infrared colors and the intensity ratios of the SiO J=1-0 v=3 to v=1&2 lines. Two overlap lines of H2O (i.e., 11(6,6) nu_2=1 -> 12(7,5) nu_2=0 and 5(0,5) nu_2=2 -> 6(3,4) nu_2=1) might explain these correlation if these overlap lines become stronger with increase of infrared colors, although the phenomena also might be explained by more fundamental ways if we take into account the variation of opacity from object to object.Comment: 49 pages, 7 figures, 3 tables, accepted for publication in ApJ. Full resolution version available at http://www.asiaa.sinica.edu.tw/~junichi/paper

Connection of Isolated Stereoclusters by Combining C-13-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum

The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R

Applications of computational geometry to the molecular simulation of interfaces

The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry, where the definition of the "shape" of a set of point is a well-known problem. In particular, we employ the $\alpha$-shape construction which, applied to the positions of the molecules, selects a shape and identifies its boundary points, which we will take to define our interfacial molecules. A single parameter needs to be fixed (the "$\alpha$" of the $\alpha$-shape), and several proposals are examined, all leading to very similar choices. Results of this methodology are evaluated against previous proposals, and seen to be reasonable.Comment: 22 pages, 8 figure

Optical Biomarkers for the Diagnosis of Osteoarthritis through Raman Spectroscopy: Radiological and Biochemical Validation Using Ex Vivo Human Cartilage Samples

[Abstract] Osteoarthritis (OA) is the most common rheumatic disease, characterized by progressive articular cartilage degradation. Raman spectroscopy (RS) has been recently proposed as a label-free tool to detect molecular changes in musculoskeletal tissues. We used cartilage samples derived from human femoral heads to perform an ex vivo study of different Raman signals and ratios, related to major and minor molecular components of articular cartilage, hereby proposed as candidate optical biomarkers for OA. Validation was performed against the radiological Kellgren–Lawrence (K-L) grading system, as a gold standard, and cross-validated against sulfated glycosaminoglycans (sGAGs) and total collagens (Hyp) biochemical contents. Our results showed a significant decrease in sGAGs (SGAGs, A1063 cm−1/A1004 cm−1) and proteoglycans (PGs, A1375 cm−1/A1004 cm−1) and a significant increase in collagen disorganization (ColD/F, A1245 cm−1/A1270 cm−1), with OA severity. These were correlated with sGAGs or Hyp contents, respectively. Moreover, the SGAGs/HA ratio (A1063 cm−1/A960 cm−1), representing a functional matrix, rich in proteoglycans, to a mineralized matrix-hydroxyapatite (HA), was significantly lower in OA cartilage (K-L I vs. III–IV, p < 0.05), whilst the mineralized to collagenous matrix ratio (HA/Col, A960 cm−1/A920 cm−1) increased, being correlated with K-L. OA samples showed signs of tissue mineralization, supported by the presence of calcium crystals-related signals, such as phosphate, carbonate, and calcium pyrophosphate dihydrate (MGP, A960 cm−1/A1004 cm−1, MGC, A1070 cm−1/A1004 cm−1 and A1050 cm−1/A1004 cm−1). Finally, we observed an increase in lipids ratio (IL, A1450 cm−1/A1670 cm−1) with OA severity. As a conclusion, we have described the molecular fingerprint of hip cartilage, validating a panel of optical biomarkers and the potential of RS as a complementary diagnostic tool for OA.Xunta de Galicia; ED431E 2018/03Xunta de Galicia; IN607A2017/1